[English] 日本語
Yorodumi- PDB-7nhk: LsaA, an antibiotic resistance ABCF, in complex with 70S ribosome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nhk | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | LsaA, an antibiotic resistance ABCF, in complex with 70S ribosome from Enterococcus faecalis | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | RIBOSOME / Antibiotic resistance element / ribosomal protein / LsaA / ABCF / target protection / antibiotic resistance | |||||||||||||||||||||
Function / homology | Function and homology information large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Crowe-McAuliffe, C. / Kasari, M. / Hauryliuk, V.H. / Wilson, D.N. | |||||||||||||||||||||
Funding support | Germany, Sweden, Estonia, 6items
| |||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya ...Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya Ignatova / Gemma C Atkinson / Alex J O'Neill / Vasili Hauryliuk / Daniel N Wilson / Abstract: Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette ...Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaA and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nhk.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nhk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nhk ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nhk | HTTPS FTP |
---|
-Related structure data
Related structure data | 12331MC 7nhlC 7nhmC 7nhnC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10682 (Title: Affinity-purified LsaA in complex with 70S ribosomes from Enterococcus faecalis Data size: 82.3 Data #1: Unaligned multi-frame micrographs of LsaA bound to 70S ribosome from Entrococcus faecalis [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 1 types, 1 molecules 0
#1: Protein | Mass: 62372.363 Da / Num. of mol.: 1 / Mutation: E142Q, E452Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: DVW78_08325 / Production host: Enterococcus faecalis (bacteria) / Strain (production host): TX5332 / References: UniProt: A0A4U4C430 |
---|
+50S ribosomal protein ... , 28 types, 28 molecules 1245678GHIJKMNOPQRSTUVWXYZF3
-RNA chain , 5 types, 5 molecules ABaDb
#9: RNA chain | Mass: 944000.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
---|---|
#10: RNA chain | Mass: 37433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
#30: RNA chain | Mass: 504170.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
#50: RNA chain | Mass: 24811.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
#51: RNA chain | Mass: 5617.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) |
-30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu
#31: Protein | Mass: 29500.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XQD8 |
---|---|
#32: Protein | Mass: 24415.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKR8 |
#33: Protein | Mass: 23273.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XRV7 |
#34: Protein | Mass: 17444.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKW0 |
#35: Protein | Mass: 11621.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKB6 |
#36: Protein | Mass: 17864.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKQ3 |
#37: Protein | Mass: 14936.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS6 |
#38: Protein | Mass: 14271.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XSA2 |
#39: Protein | Mass: 11731.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKR5 |
#40: Protein | Mass: 13739.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKV1 |
#41: Protein | Mass: 15309.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKQ7 |
#42: Protein | Mass: 13595.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKT7 |
#43: Protein | Mass: 7172.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKT0 |
#44: Protein | Mass: 10668.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XRW3 |
#45: Protein | Mass: 10356.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XP69 |
#46: Protein | Mass: 10332.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS3 |
#47: Protein | Mass: 9262.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKB3 |
#48: Protein | Mass: 10586.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XKS0 |
#49: Protein | Mass: 8972.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: A0A1B4XQJ7 |
-Non-polymers , 5 types, 185 molecules
#54: Chemical | #55: Chemical | ChemComp-MG / #56: Chemical | #57: Chemical | ChemComp-K / #58: Chemical | ChemComp-PUT / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: LsaA-in complex with 70S ribosome, mRNA, and tRNA / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL |
---|---|
Molecular weight | Value: 2.2 MDa / Experimental value: NO |
Source (natural) | Organism: Enterococcus faecalis (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 5s blotting |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: -2200 nm / Nominal defocus min: -700 nm / Cs: 2.7 mm |
Image recording | Electron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59262 / Symmetry type: POINT |